So I know this is pretty late and I am not sure if this is THE source of your problem however it warrants pointing out:
it looks like you tried to use a bowtie 1 index with tophat 2 without telling tophat that you are giving it the old type of index. If you want to do this you must pass tophat the "--bowtie1" switch so that it knows how to handle the indexes. Bowtie 2 indexes are not interchangeable with bowtie 1.
it looks like you tried to use a bowtie 1 index with tophat 2 without telling tophat that you are giving it the old type of index. If you want to do this you must pass tophat the "--bowtie1" switch so that it knows how to handle the indexes. Bowtie 2 indexes are not interchangeable with bowtie 1.
Hello, This is my first post.
i am using Tophat 2.0.6 with Bowtie 0.12 and i am trying to run this command on my clusters:
Quote:
tophat -o /fastspace/bioinfo_projects/asfaw_degu/th2_CS21_2 -i 10 -I 11000 --min-coverage-intron 10 --max-coverage-intron 11000 --min-segment-intron 10 --max-segment-intron 11000 -p 22 -G /storage16/projects/asfaw_degu/02.genome/Vitis_vinifera.IGGP_12x.15.gtf -M /storage16/projects/asfaw_degu/02.genome/Vitis_vinifera /storage16/projects/asfaw_degu/01.fastq/00.Project_Aaron_Fait/Sample_CS_21/R1/CS_21_TAGCTT_L006_R1.fastq /storage16/projects/asfaw_degu/01.fastq/00.Project_Aaron_Fait/Sample_CS_21/R2/CS_21_TAGCTT_L006_R2.fastq
i am using Tophat 2.0.6 with Bowtie 0.12 and i am trying to run this command on my clusters:
Quote:
tophat -o /fastspace/bioinfo_projects/asfaw_degu/th2_CS21_2 -i 10 -I 11000 --min-coverage-intron 10 --max-coverage-intron 11000 --min-segment-intron 10 --max-segment-intron 11000 -p 22 -G /storage16/projects/asfaw_degu/02.genome/Vitis_vinifera.IGGP_12x.15.gtf -M /storage16/projects/asfaw_degu/02.genome/Vitis_vinifera /storage16/projects/asfaw_degu/01.fastq/00.Project_Aaron_Fait/Sample_CS_21/R1/CS_21_TAGCTT_L006_R1.fastq /storage16/projects/asfaw_degu/01.fastq/00.Project_Aaron_Fait/Sample_CS_21/R2/CS_21_TAGCTT_L006_R2.fastq
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